Figuring out HiC restriction enzyme

Question

[gbdias]

Hi,

Does anyone have a strategy for figuring out which restriction enzyme was utilized in a HiC experiment based on the Illumina reads alone?

Thanks

Answer 1

[gbdias]

Figured it out by checking the overrepresented k-mers at the FASTQC report for my data.

[joneill4x]

Can you go into further detail how you figured it out gbdias? I am in the same situation as you were. There are 20 over-represented 7-mers located near the start of my reads. (Both for forward reads and reverse reads). How do I used this data to deduce the restriction enzyme cutting site?

[Devon Ryan]

Check if the first 2-3 bases are common and then make a palindrome of that. For example, if the k-mers tend to start with TC then GATC is the cut site and DpnII was used.

[nkmalini97]

@gbdias I have tried this approach. I have got the fastqc file reports. I get the k-mers that start with GATC or other enzyme's cut site (example:HindIII-AGCTT (A^AGCTT)) without having to generate a palindrome with the first 2-3 common bases. I was wondering if I can consider the enzyme from the k-mers which are mostly the appropriate cut sites. Is there any reference or standard with which we can be sure that the overrepresented sequences contain the k-mers of the enzyme restriction sites. I would want to know why we consider the overrepresented sequences in particular